recipe bioconductor-tvtb

TVTB: The VCF Tool Box

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/TVTB.html

License:

Artistic-2.0

Recipe:

/bioconductor-tvtb/meta.yaml

The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).

package bioconductor-tvtb

versions:

1.32.0-0,  1.28.0-0,  1.26.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0, 

1.32.0-0,  1.28.0-0,  1.26.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0

depends bioconductor-annotationfilter:

>=1.30.0,<1.31.0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0

depends bioconductor-ensembldb:

>=2.30.0,<2.31.0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-gviz:

>=1.50.0,<1.51.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-limma:

>=3.62.0,<3.63.0

depends bioconductor-rsamtools:

>=2.22.0,<2.23.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends bioconductor-variantannotation:

>=1.52.0,<1.53.0

depends r-base:

>=4.4,<4.5.0a0

depends r-ggally:

depends r-ggplot2:

depends r-reshape2:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-tvtb

and update with::

   mamba update bioconductor-tvtb

To create a new environment, run:

mamba create --name myenvname bioconductor-tvtb

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-tvtb:<tag>

(see `bioconductor-tvtb/tags`_ for valid values for ``<tag>``)

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